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Enhanced, improved and novel NMDC workflows to advance microbiome science
Similar to the entire field of genomics, all NMDC workflows (Appendix 15) are subject to an iterative
improvement process. To …
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Hi Kraken2 devs!
I'm hoping to get some recommendations for best practices for the Kraken2 input fastqs.
My questions are as follows:
1) should reads be trimmed before Kraken2?
2) should reads…
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https://github.com/waldronlab/MicrobiomeWorkshop with @katiasmirn and @zhaoni153
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Hello,
I was hoping you might have some advice about understanding an issue I am running into with some microbiome samples (fungal community in soybean at ITS region).
The issue has to do with i…
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The workflow and tutorial queries (https://training.galaxyproject.org/training-material/workflows/embed.html?query=microbiome) via the GTN are useful to filter for specific communities and are already…
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I encountered an issue when running qadabra, it has to do with two of the tools that are used by qadabra; corncob and metagenomeseq. I checked both log files (see underneath), but it was not clear to …
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https://www.nature.com/nbt/journal/v35/n5/full/nbt.3790.html - Discovering and linking public omics data sets using the Omics Discovery Index
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- dada2: https://benjjneb.github.io/dada2/tutorial.html The tutorial is for R, but since the Galaxy tools wrap the R functions 1:1 it should be easy to follow.
- qiime2: https://docs.qiime2.org/jupy…
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New error when running taxonomy
**Command:**
cd $tmp
in_dir=/projects/cmi_proj/blood_microbiome/niaid/combined
out_root=$in_dir/shogun
align_dir=$out_root/wol_alignments
taxonomy=/projects/c…
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Hi,
I have a question regarding the "All_gene_collections_mapped.depth.txt" output file.
Have the values provided for the estimate coverage of each contig **normalised** or **scaled** by the wo…